I do not know the circumstances under which this happened, or how it could even happen. At the time, I thought it likely a visual bug, but I see this morning it is still the same.
Last night, I had been swapping out skill lines on one of my nightblades, and using the shrine, I noticed that "Impale" had a lock symbol over it, which I thought was weird. So I took the points out of it (it already had 2 points in, lol) and it showed me that Assassin's Blade was at level 1.

I just did daily crafting writs on this particular toon, and now it is at rank 2 of the BASE morph.
I don't like wasting XP from crafting writs, so years ago I had actually made a spreadsheet to track each my toons progress on every skill line. All of my toons have all of their base class skills with both morphs maxed. Checking my spreadsheet for this particular toon, yes, it confirms it for me.
I personally don't care much about re-leveling it, I still have Master Writs left, but there is clearly some sort of situational bug that can have players lose progress in their skill lines.
PC-NA